TrajectoryUtils

This is the development version of TrajectoryUtils; for the stable release version, see TrajectoryUtils.

Single-Cell Trajectory Analysis Utilities

Bioconductor version: Development (3.22)

Implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.

Author: Aaron Lun [aut, cre], Kelly Street [aut]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("TrajectoryUtils")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("TrajectoryUtils")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TrajectoryUtils")

Trajectory utilities	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, SingleCell, Software
Version	1.17.0
In Bioconductor since	BioC 3.13 (R-4.1) (4.5 years)
License	GPL-3
Depends	SingleCellExperiment
Imports	methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment
System Requirements
URL	https://bioconductor.org/packages/TrajectoryUtils
Bug Reports	https://github.com/LTLA/TrajectoryUtils/issues

Suggests	BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown
Linking To
Enhances
Depends On Me	slingshot, TSCAN
Imports Me	condiments, singleCellTK, tradeSeq
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	TrajectoryUtils_1.17.0.tar.gz
Windows Binary (x86_64)	TrajectoryUtils_1.17.0.zip
macOS Binary (x86_64)	TrajectoryUtils_1.17.0.tgz
macOS Binary (arm64)	TrajectoryUtils_1.17.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TrajectoryUtils
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TrajectoryUtils
Bioc Package Browser	https://code.bioconductor.org/browse/TrajectoryUtils/
Package Short Url	https://bioconductor.org/packages/TrajectoryUtils/
Package Downloads Report	Download Stats